Last updated: 2024-04-16

Checks: 7 0

Knit directory: SuSiE-ASH/

This reproducible R Markdown analysis was created with workflowr (version 1.7.1). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.


Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

The command set.seed(20240328) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version 9f85745. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:


Ignored files:
    Ignored:    .DS_Store
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    analysis/.DS_Store
    Ignored:    code/.DS_Store
    Ignored:    code/SuSiE-ASH-Versions/.DS_Store
    Ignored:    submodules/.DS_Store

Untracked files:
    Untracked:  Genotype-Matrix.R
    Untracked:  X20
    Untracked:  attainable-R-test.html
    Untracked:  large_simulation_1.4to1_L10_0.01nonsparse.RData
    Untracked:  large_simulation_1.4to1_L10_0.05nonsparse.RData
    Untracked:  large_simulation_1.4to1_L20_0.01nonsparse.RData
    Untracked:  large_simulation_1.4to1_L20_0.05nonsparse.RData
    Untracked:  large_simulation_1.4to1_L30_0.01nonsparse.RData
    Untracked:  large_simulation_1.4to1_L30_0.05nonsparse.RData
    Untracked:  large_simulation_3to1_L10_0.01nonsparse.RData
    Untracked:  large_simulation_3to1_L10_0.05nonsparse.RData
    Untracked:  large_simulation_3to1_L20_0.01nonsparse.RData
    Untracked:  large_simulation_3to1_L20_0.05nonsparse.RData
    Untracked:  large_simulation_3to1_L30_0.01nonsparse.RData
    Untracked:  large_simulation_3to1_L30_0.05nonsparse.RData
    Untracked:  large_simulation_5to1_L10_0.01nonsparse.RData
    Untracked:  large_simulation_5to1_L10_0.05nonsparse.RData
    Untracked:  large_simulation_5to1_L20_0.01nonsparse.RData
    Untracked:  large_simulation_5to1_L20_0.05nonsparse.RData
    Untracked:  large_simulation_5to1_L30_0.01nonsparse.RData
    Untracked:  large_simulation_5to1_L30_0.05nonsparse.RData
    Untracked:  site_libs/

Unstaged changes:
    Modified:   Simulation-Final.Rmd
    Modified:   analysis/Simulation.Rmd
    Modified:   attainable-R-test.Rmd
    Modified:   code/SuSiE-ASH-Versions/susie-ash-warmstart-v2.R
    Modified:   submodules/susieR

Staged changes:
    Deleted:    analysis/Non-Sparse Simulation.Rmd

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.


These are the previous versions of the repository in which changes were made to the R Markdown (analysis/Simulation-Results.Rmd) and HTML (docs/Simulation-Results.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File Version Author Date Message
Rmd 9f85745 alexmccreight 2024-04-16 move folder

1.4:1 Theta to Beta Ratio

Model CS_FDR CS_Recall CS_Size Coverage L nonsparse_coverage theta_beta_ratio
SuSiE 0.123 0.126 8.456 0.869 10 0.01 1.4
SuSiE-Attainable 0.095 0.133 6.849 0.896 10 0.01 1.4
SuSiE-ASH 0.127 0.121 8.250 0.865 10 0.01 1.4
SuSiE 0.137 0.198 11.149 0.842 20 0.01 1.4
SuSiE-Attainable 0.157 0.156 6.138 0.837 20 0.01 1.4
SuSiE-ASH 0.117 0.117 10.519 0.858 20 0.01 1.4
SuSiE 0.076 0.162 13.516 0.915 30 0.01 1.4
SuSiE-Attainable 0.091 0.121 5.757 0.904 30 0.01 1.4
SuSiE-ASH 0.089 0.085 14.411 0.904 30 0.01 1.4
SuSiE 0.069 0.046 22.428 0.871 10 0.05 1.4
SuSiE-Attainable 0.094 0.026 9.180 0.854 10 0.05 1.4
SuSiE-ASH 0.094 0.033 20.391 0.849 10 0.05 1.4
SuSiE 0.118 0.043 15.620 0.810 20 0.05 1.4
SuSiE-Attainable 0.190 0.025 7.997 0.759 20 0.05 1.4
SuSiE-ASH 0.108 0.039 15.596 0.819 20 0.05 1.4
SuSiE 0.091 0.030 12.145 0.891 30 0.05 1.4
SuSiE-Attainable 0.111 0.022 7.258 0.873 30 0.05 1.4
SuSiE-ASH 0.081 0.023 11.560 0.904 30 0.05 1.4

3:1 Theta to Beta Ratio

Model CS_FDR CS_Recall CS_Size Coverage L nonsparse_coverage theta_beta_ratio
SuSiE 0.144 0.130 9.665 0.851 10 0.01 3
SuSiE-Attainable 0.150 0.127 6.725 0.850 10 0.01 3
SuSiE-ASH 0.146 0.121 10.521 0.849 10 0.01 3
SuSiE 0.102 0.226 11.958 0.890 20 0.01 3
SuSiE-Attainable 0.091 0.202 6.692 0.902 20 0.01 3
SuSiE-ASH 0.080 0.180 12.193 0.913 20 0.01 3
SuSiE 0.217 0.152 18.494 0.764 30 0.01 3
SuSiE-Attainable 0.200 0.105 5.213 0.775 30 0.01 3
SuSiE-ASH 0.217 0.152 19.192 0.764 30 0.01 3
SuSiE 0.133 0.039 16.400 0.800 10 0.05 3
SuSiE-Attainable 0.168 0.032 9.685 0.754 10 0.05 3
SuSiE-ASH 0.147 0.037 15.662 0.782 10 0.05 3
SuSiE 0.154 0.041 12.852 0.771 20 0.05 3
SuSiE-Attainable 0.184 0.030 8.996 0.766 20 0.05 3
SuSiE-ASH 0.168 0.032 13.984 0.760 20 0.05 3
SuSiE 0.144 0.033 13.730 0.786 30 0.05 3
SuSiE-Attainable 0.256 0.018 6.864 0.725 30 0.05 3
SuSiE-ASH 0.117 0.027 11.986 0.850 30 0.05 3

5:1 Theta to Beta Ratio

Model CS_FDR CS_Recall CS_Size Coverage L nonsparse_coverage theta_beta_ratio
SuSiE 0.163 0.124 10.992 0.824 10 0.01 5
SuSiE-Attainable 0.153 0.123 6.790 0.829 10 0.01 5
SuSiE-ASH 0.187 0.115 11.095 0.799 10 0.01 5
SuSiE 0.099 0.220 12.555 0.897 20 0.01 5
SuSiE-Attainable 0.103 0.182 7.813 0.894 20 0.01 5
SuSiE-ASH 0.092 0.158 12.139 0.903 20 0.01 5
SuSiE 0.137 0.185 12.182 0.855 30 0.01 5
SuSiE-Attainable 0.159 0.147 6.476 0.832 30 0.01 5
SuSiE-ASH 0.139 0.148 12.037 0.851 30 0.01 5
SuSiE 0.102 0.041 13.920 0.856 10 0.05 5
SuSiE-Attainable 0.145 0.025 7.719 0.830 10 0.05 5
SuSiE-ASH 0.093 0.038 14.280 0.849 10 0.05 5
SuSiE 0.123 0.048 15.740 0.810 20 0.05 5
SuSiE-Attainable 0.167 0.028 8.116 0.786 20 0.05 5
SuSiE-ASH 0.138 0.038 16.158 0.778 20 0.05 5
SuSiE 0.139 0.041 15.056 0.778 30 0.05 5
SuSiE-Attainable 0.190 0.026 7.576 0.752 30 0.05 5
SuSiE-ASH 0.152 0.034 13.380 0.765 30 0.05 5

sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.1

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] lubridate_1.9.3 forcats_1.0.0   stringr_1.5.1   dplyr_1.1.4    
 [5] purrr_1.0.2     readr_2.1.5     tidyr_1.3.1     tibble_3.2.1   
 [9] ggplot2_3.5.0   tidyverse_2.0.0

loaded via a namespace (and not attached):
 [1] sass_0.4.9        utf8_1.2.4        generics_0.1.3    stringi_1.8.3    
 [5] hms_1.1.3         digest_0.6.35     magrittr_2.0.3    timechange_0.3.0 
 [9] evaluate_0.23     grid_4.3.1        fastmap_1.1.1     rprojroot_2.0.4  
[13] workflowr_1.7.1   jsonlite_1.8.8    whisker_0.4.1     promises_1.3.0   
[17] fansi_1.0.6       scales_1.3.0      jquerylib_0.1.4   cli_3.6.2        
[21] rlang_1.1.3       munsell_0.5.1     withr_3.0.0       cachem_1.0.8     
[25] yaml_2.3.8        tools_4.3.1       tzdb_0.4.0        colorspace_2.1-0 
[29] httpuv_1.6.15     vctrs_0.6.5       R6_2.5.1          lifecycle_1.0.4  
[33] git2r_0.33.0      fs_1.6.3          pkgconfig_2.0.3   pillar_1.9.0     
[37] bslib_0.7.0       later_1.3.2       gtable_0.3.4      glue_1.7.0       
[41] Rcpp_1.0.12       xfun_0.43         tidyselect_1.2.1  rstudioapi_0.16.0
[45] knitr_1.45        htmltools_0.5.8.1 rmarkdown_2.26    compiler_4.3.1